De novo designed binders targeting human epcam and pdl1 receptors

Abstract

Disclosed herein are polypeptides that bind to the epithelial cell adhesion molecule (EpCAM) and programmed death-ligand I (PDL 1) receptors, nucleic acids encoding them, and methods for their use in treating or limited development of cancer, auto immune disease, or inflammation. The disclosure further provides nucleic acids encoding a polypeptide of the disclosure: expression vector comprising a nucleic acid of the disclosure operatively linker to a suitable regulatory control element, host cells comprising a polypeptide, fusion protein, nucleic acid, or expression vector of any embodiment of the disclosure, and pharmaceutical compositions, comprising the polypeptide, fusion protein, nucleic acid, expression vector, or host cell of any embodiment; and a pharmaceutically acceptable carrier.

1 . A polypeptide that
 (a) binds to human epithelial cell adhesion molecule (EpCAM) receptor, wherein the polypeptide comprises the amino acid sequence of SEQ ID NO:1; or   (b) binds to human EpCAM receptor, wherein the polypeptide comprises the amino acid sequence of SEQ ID NO:2; or   (c) binds to human programmed death-ligand 1 (PDL1) receptor, wherein the polypeptide comprises the amino acid sequence of SEQ ID NO:3.   
     
     
         2 . The polypeptide of  claim 1 , wherein interface residues 21, 22, 24, 25, 28, 29, 32, 33, 36, 42, 45, 46, 49, 50, 52, 53, 54, and 57 relative to SEQ ID NO:1 are selected from the corresponding interface residues present in any one of SEQ ID NO:4-18. 
     
     
         3 . The polypeptide of  claim 1 , comprising an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from SEQ ID NO:4-18. 
     
     
         4 .- 8 . (canceled) 
     
     
         9 . The polypeptide of claim  19 , wherein interface residues 1, 4, 5, 7, 8, 9, 11, 12, 15, 16, 19, 20, 43, 44, 45, 47, 48, 50, 51, 52, 54, and 55 relative to SEQ ID NO:2 are selected from the interface residues present in the amino acid sequence selected from SEQ ID NO:19-21. 
     
     
         10 . The polypeptide of  claim 9 , comprising an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from SEQ ID NO:19-21. 
     
     
         11 .- 12 . (canceled) 
     
     
         13 . The polypeptide of  claim 1 , wherein residues 1-20 relative to SEQ ID NO:2 form a first alpha-helix, residues 24-41 relative to SEQ ID NO:2 form a second alpha-helix, and residues 44-57 relative to SEQ ID NO:2 form a third alpha-helix. 
     
     
         14 . The polypeptide of  claim 13 , wherein alpha-helical residues are identical to the reference sequence alpha-helical residues. 
     
     
         15 . (canceled) 
     
     
         16 . The polypeptide of  claim 1 , wherein interface residues 1, 4, 5, 8, 11, 12, 15, 16, 19, 42, 43, 44, 47, 48, 51, 52, 54, 55, and 56 relative to SEQ ID NO:3 are selected from the interface residues present in the amino acid sequences selected from SEQ ID NO:22-30. 
     
     
         17 . The polypeptide of  claim 16 , comprising an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from SEQ ID NO:22-30. 
     
     
         18 .- 19 . (canceled) 
     
     
         20 . The polypeptide of  claim 16 , wherein residues 1-20 relative to SEQ ID NO:3 form a first alpha-helix, residues, residues 24-41 relative to SEQ ID NO:3 form a second alpha-helix, and residues 44-55 relative to SEQ ID NO:3 form a third alpha-helix. 
     
     
         21 .- 22 . (canceled) 
     
     
         23 . A fusion protein comprising 2, 3, 4, or more polypeptides according to  claim 1 , wherein the polypeptides may be directly linked, or may be linked via an amino acid linker. 
     
     
         24 . A nucleic acid encoding the polypeptide of  claim 1 . 
     
     
         25 . An expression vector comprising the nucleic acid of  claim 24  operatively linker to a suitable regulatory control element. 
     
     
         26 . A host cell comprising the expression vector of  claim 25 . 
     
     
         27 . A pharmaceutical composition, comprising:
 (a) the polypeptide of  claim 1 ; and   (b) a pharmaceutically acceptable carrier.   
     
     
         28 . (canceled) 
     
     
         29 . A method for treating or limiting development of cancer, autoimmune disease, or inflammation, comprising administering to a subject in need thereof an amount effective of the polypeptide of  claim 1  to treat or limit development of the disorder.